Precise, species-level identification of plants in foods and dietary supplements is difficult. While the use of DNA barcoding regions (short regions of DNA with diagnostic utility) has been effective for many inquiries, it is not always a robust approach for closely related species, especially in highly processed products. The use of fully sequenced chloroplast genomes, as an alternative to short diagnostic barcoding regions, has demonstrated utility for closely related species. The U. S. Food and Drug Administration (FDA) has also developed species-specific DNA-based assays targeting plant species of interest by utilizing chloroplast genome sequences. Here, we introduce a repository of complete chloroplast genome sequences called GenomeTrakrCP, which will be publicly available at the National Center for Biotechnology Information (NCBI). Target species for inclusion are plants found in foods and dietary supplements, toxin producers, common contaminants and adulterants, and their close relatives. Publicly available data will include annotated assemblies, raw sequencing data, and voucher information with each NCBI accession associated with an authenticated reference herbarium specimen. To date, 40 complete chloroplast genomes have been deposited in GenomeTrakrCP (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA325670/), and this will be expanded in the future.

The large-flowered parasitic genus Rafflesia R.Br. (Rafflesiaceae) has long fascinated naturalists and scientists and is an iconic symbol for plant conservation. Techniques to effectively propagate members of the genus outside of their natural habitat are sparse, and grafting infected Tetrastigma K.Schum.(Vitaceae) host plants has previously been reported as a successful strategy for ex situ conservation of Rafflesia. Here we report our attempts in the United States to propagate host cuttings infected with Rafflesia speciosa Barcelona & Fernando and R. lagascae Blanco collectedfrom the Philippines, as well as uninfected host material. We also describe efforts to germinate R. speciosa seeds in vitro using various plant growth regulators (PGRs). After rooting, infected host cuttings survived for a maximum of 11 months, but did not produce shoots. However, an uninfected cutting of T. cf. magnum grafted onto an established Malaysian species of Tetrastigma in June 2017 has succeeded in the commencement of new growth. Three propagules of a second potential host, T. harmandii Planch., have also been vigorously growing at the United States Botanic Garden since June 2017. However, Rafflesia seeds did not germinate with the application of PGRs, even though the seeds were viable according to tetrazolium (TZ) testing.These ex situ propagation attempts have revealed challenges in propagating these species outside of their native ranges, but our incremental success in rooting infected Tetrastigma, as well as grafting interspecific Tetrastigma species, bodes well for further advances. With Philippine host species, T. harmandii and T. cf. magnum in cultivation, we can begin using these specimens for future experimentation involving grafting of infected material and Rafflesia seed inoculation trials.Furthermore, we describe new avenues of propagation techniques for Rafflesia as practised by Marius Gabin, one of the owners of the Vivian Rafflesia garden, which contains a natural Rafflesia forest habitat at Poring Springs, Sabah, Malaysia. Gabin openly shared his successes in artificially inoculating Rafflesia seeds into a mature Tetrastigma vine. Gabin’s willingness to share his experience highlights the importance of collaborating with practitioners who have developed local knowledge of Rafflesia horticulture and conservation.

Banisteriopsis caapi is a native South American vine that has been used for centuries by certain tribes along the Amazon basin to treat illnesses. In this study, we present the fully annotated chloroplast genome of Banisteriopsis caapi.

Societal Impact StatementRafflesia is a genus of parasitic plants with the largest flowers in the world, unique to the threatened forest habitats of tropical Asia. Here, we report on genes that are active (the transcriptome) in Rafflesia seeds as part of a larger effort to understand Rafflesia. Rafflesia has never been grown successfully outside of its native range. Consequently, seed banking is not yet possible, precluding a critical management strategy for conservation. The study of Rafflesia seed biology is a critical step to improve its cultivation, which will educate the public about unique species and the importance of conserving their habitats.Summary Rafflesia is of great interest as one of the only two plants known to have completely lost its chloroplast genome. Rafflesia is a holoparasite and an endophyte that lives inside the tissues of its host, a tropical grape vine (Tetrastigma), emerging only to bloom—with the largest flower of any plant. Here, we report the first Rafflesia seed transcriptome and compare it with those of other plants to deepen our understanding of its extraordinary life history. We assembled a transcriptome from RNA extracted from seeds of the Philippine endemic Rafflesia speciosa and compared this with those of other plants, including Arabidopsis, parasitic plants Striga and Cuscuta, and the mycoheterotrophic orchid Anoectochilus. Genetic and metabolic seed pathways in Rafflesia were generally similar to the other plant species. However, there were some notable exceptions. We found evidence of horizontal transfer of a gene potentially involved in circumventing host defenses. Moreover, we identified a possible convergence among parasitic plants because Rafflesia, Striga, and Cuscuta shared important similarities. We were unable to find evidence of genes involved in mycorrhizal symbiosis, suggesting that mycoheterotrophy is unlikely to play a role in Rafflesia parasitism. To date, ex situ propagation of Rafflesia by seed has been mostly unsuccessful. Our research is a bold step forward in understanding the fundamentals of Rafflesia seed biology that will inform the continued propagation and seed‐banking efforts concerning this recalcitrant plant. We discuss our findings in the broader context of the conservation of a genus in peril.

Main conclusion Metabolites in Rafflesia-infected and non-infected Tetrastigma were compared which may have applications in Rafflesia propagation. Benzylisoquinoline alkaloids, here reported for the first time in Vitaceae, were abundant in non-infected shoots and may be a form of defense. In Rafflesia-infected shoots, oxylipins, which mediate immune response, were elevated. Abstract Endemic to the forests of Southeast Asia, Rafflesia (Rafflesiaceae) is a genus of holoparasitic plants producing the largest flowers in the world, yet completely dependent on its host, the tropical grape vine, Tetrastigma. Rafflesia species are threatened with extinction, making them an iconic symbol of plant conservation. Thus far, propagation has proved challenging, greatly decreasing efficacy of conservation efforts. This study compared the metabolites in the shoots of Rafflesia-infected and non-infected Tetrastigma loheri to examine how Rafflesia infection affects host metabolomics and elucidate the Rafflesia infection process. Results from LC–MS-based untargeted metabolomics analysis showed benzylisoquinoline alkaloids were naturally more abundant in non-infected shoots and are here reported for the first time in the genus Tetrastigma, and in the grape family, Vitaceae. These metabolites have been implicated in plant defense mechanisms and may prevent a Rafflesia infection. In Rafflesia-infected shoots, oxygenated fatty acids, or oxylipins, and a flavonoid, previously shown involved in plant immune response, were significantly elevated. This study provides a preliminary assessment of metabolites that differ between Rafflesia-infected and non-infected Tetrastigma hosts and may have applications in Rafflesia propagation to meet conservation goals.